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Question: Problem with biomart's listMarts function
3
gravatar for Johannes Rainer
2.0 years ago by
Johannes Rainer1.1k
Italy
Johannes Rainer1.1k wrote:

dear All,

was there any change to the biomart web service recently? Today I stumbled over the following problem when I wanted to list all available marts:

> library(biomaRt)
> listMarts()
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2
>


I guess something had changed at the biomart web service.

 

cheers, jo

 

My R/Bioconductor:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.26.0

loaded via a namespace (and not attached):
 [1] IRanges_2.4.1        parallel_3.2.2       DBI_0.3.1           
 [4] RCurl_1.95-4.7       Biobase_2.30.0       AnnotationDbi_1.32.0
 [7] RSQLite_1.0.0        S4Vectors_0.8.1      BiocGenerics_0.16.1
[10] stats4_3.2.2         bitops_1.0-6         XML_3.98-1.3        

 

ADD COMMENTlink modified 18 months ago by Paul Shannon360 • written 2.0 years ago by Johannes Rainer1.1k

I also get the same error, as well as apparently some other users

ADD REPLYlink written 2.0 years ago by Assa Yeroslaviz1.3k

the portal biomart.org said also that it is not avaiable.

ADD REPLYlink written 2.0 years ago by Assa Yeroslaviz1.3k
7
gravatar for Assa Yeroslaviz
2.0 years ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

as the main portal is not available, you need to specify one their other serers.

this is working (mouse mart, but changeable):

ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host = "jul2015.archive.ensembl.org")

this uses the latest archived version, Ensembl 81 (http://jul2015.archive.ensembl.org/index.html)

Assa

ADD COMMENTlink written 2.0 years ago by Assa Yeroslaviz1.3k

Thanks, this was very helpful. Using the host "ensembl.org" gives you the latest genomes, but you can access older versions using archives. In the first example, I retrieve information for mm9. In the second example, I use a special host for hg19. See also http://useast.ensembl.org/info/website/archives/index.html

mouse <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "may2012.archive.ensembl.org")

human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "grch37.ensembl.org")
ADD REPLYlink modified 18 months ago • written 18 months ago by petervangalen0
3
gravatar for Johannes Rainer
2.0 years ago by
Johannes Rainer1.1k
Italy
Johannes Rainer1.1k wrote:

OK, finally managed to have a look at the News page at www.biomart.org and there is stated:

If you are a user of biomaRt (a part of the Bioconductor library) change the host from 'www.biomart.org' to 'www.ensembl.org'. Similar procedure can be used for all the other community servers.

Basically, using

> listMarts(host="www.ensembl.org")

               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

 

everything works again...

 

ADD COMMENTlink written 2.0 years ago by Johannes Rainer1.1k

Hi,

I cannot get it work for www.metazoa.ensembl.org. I know the data set I need is there, any idea on how I can access it?

Thank you for your help,

list2=listMarts(host="www.metazoa.ensembl.org")

Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'nbsp' not defined
Entity 'raquo' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'middot' not defined
Entity 'middot' not defined
Opening and ending tag mismatch: p line 200 and select
Opening and ending tag mismatch: form line 198 and p
Opening and ending tag mismatch: div line 197 and form
Opening and ending tag mismatch: input line 78 and div
Entity 'copy' not defined
Entity 'nbsp' not defined
Entity 'nbsp' not defined
Entity 'nbsp' not defined
Error: 1: Entity 'hellip' not defined
2: Entity 'hellip' not defined
3: Entity 'nbsp' not defined
4: Entity 'raquo' not defined
5: Entity 'hellip' not defined
6: Entity 'hellip' not defined
7: Entity 'hellip' not defined
8: Entity 'hellip' not defined
9: Entity 'middot' not defined
10: Entity 'middot' not defined
11: Opening and ending tag mismatch: p line 200 and select
12: Opening and ending tag mismatch: form line 198 and p
13: Opening and ending tag mismatch: div line 197 and form
14: Opening and ending tag mismatch: input line 78 and div
15: Entity 'copy' not defined
16: Entity 'nbsp' not defined
17: Entity 'nbsp' not defined
18: Entity 'nbsp' not defined
ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Matarit0

Skip the "www":

listMarts(host="metazoa.ensembl.org")
ADD REPLYlink written 2.0 years ago by Johannes Rainer1.1k

Thanks! It works. I would not have thought about that as www was not an issue for ensembl.org.

ADD REPLYlink written 2.0 years ago by Matarit0
1
gravatar for hygine
2.0 years ago by
hygine140
beijing
hygine140 wrote:

3 type have changed in use:

listMarts(host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="aplatyrhynchos_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="drerio_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="ggallus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="oaries_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="rnorvegicus_gene_ensembl", host="www.ensembl.org")

useMart("ENSEMBL_MART_ENSEMBL",dataset="sscrofa_gene_ensembl", host="www.ensembl.org")

 

listMarts(host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="bmori_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="amellifera_eg_gene", host="metazoa.ensembl.org")

useMart("metazoa_mart",dataset="cgigas_eg_gene", host="metazoa.ensembl.org")

 

listMarts(host="plants.ensembl.org")

useMart("plants_mart",dataset="zmays_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="sbicolor_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="stuberosum_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="osativa_eg_gene", host="plants.ensembl.org")

useMart("plants_mart",dataset="creinhardtii_eg_gene", host="plants.ensembl.org")

ADD COMMENTlink written 2.0 years ago by hygine140
1
gravatar for ashley.doane
19 months ago by
ashley.doane20
United States
ashley.doane20 wrote:

This seems to be not working again.  Please share if you know a solution!

> library(biomaRt)

> ensembl=useMart("ensembl")

> ensembl=useMart("ensembl")

​Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing

 

 

> listMarts(host="www.ensembl.org")

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing

 

 sessionInfo()
R version 3.3.0 beta (2016-04-10 r70465)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

 

 

 

 

 

ADD COMMENTlink written 19 months ago by ashley.doane20

I can confirm that this is occurring on both the devel and stable biomaRts on both windows and mac, hopefully the host is just temporarily down, as a work around if you don't mind using old annotations try the dec 2015 ensembl archive?

#doesn't work (same as "www.ensembl.org")

> biomaRt::listMarts(host="mar2016.archive.ensembl.org")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing

# works
> biomaRt::listMarts(host="dec2015.archive.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 83
2     ENSEMBL_MART_SNP  Ensembl Variation 83
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 83
4    ENSEMBL_MART_VEGA               Vega 63
5                pride        PRIDE (EBI UK)

ADD REPLYlink modified 19 months ago • written 19 months ago by zskidmor10
1

on the surface at least it seems like my suspicions were right, going to www.ensembl.org and clicking on the biomart link will verify that the service is temporarily unavailable, but works for the archives.

ADD REPLYlink written 19 months ago by zskidmor10
0
gravatar for Mnoon
19 months ago by
Mnoon10
Mnoon10 wrote:

its still not working for me.. Here is what I get:

> ensembl.human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",  host = "www.ensembl.org" )
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined

 

ADD COMMENTlink written 19 months ago by Mnoon10

Just a very wild guess, try setting

options(useFancyQuotes=FALSE)

in your R session.

If not, can you please provide the output of your sessionInfo() ? Eventually this was just some temporary problem on their side, since it is working for me with

> sessionInfo()
R version 3.3.0 beta (2016-04-17 r70499)
Platform: x86_64-apple-darwin15.5.0/x86_64 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.27.2

loaded via a namespace (and not attached):
 [1] IRanges_2.5.46        parallel_3.3.0        DBI_0.3.1            
 [4] RCurl_1.95-4.8        Biobase_2.31.3        AnnotationDbi_1.33.14
 [7] RSQLite_1.0.0         S4Vectors_0.9.52      BiocGenerics_0.17.5  
[10] stats4_3.3.0          bitops_1.0-6          XML_3.98-1.4         

 

ADD REPLYlink modified 19 months ago • written 19 months ago by Johannes Rainer1.1k

Hi Johannes, 

I tried " options(useFancyQuotes=FALSE)" and got the error below.

> options(useFancyQuotes=FALSE)

> ensembl.human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",  host = "www.ensembl.org" )
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined

Here is the Session Info:

> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1 biomaRt_2.26.1      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4                RColorBrewer_1.1-2         futile.logger_1.4.1       
 [4] GenomeInfoDb_1.6.3         plyr_1.8.3                 XVector_0.10.0            
 [7] bitops_1.0-6               futile.options_1.0.0       tools_3.2.4               
[10] zlibbioc_1.16.0            rpart_4.1-10               RSQLite_1.0.0             
[13] annotate_1.48.0            gtable_0.2.0               lattice_0.20-33           
[16] DBI_0.4                    parallel_3.2.4             RcppArmadillo_0.6.700.3.0 
[19] gridExtra_2.2.1            genefilter_1.52.1          cluster_2.0.4             
[22] S4Vectors_0.8.11           IRanges_2.4.8              locfit_1.5-9.1            
[25] stats4_3.2.4               grid_3.2.4                 nnet_7.3-12               
[28] Biobase_2.30.0             AnnotationDbi_1.32.3       XML_3.98-1.4              
[31] survival_2.39-2            BiocParallel_1.4.3         foreign_0.8-66            
[34] latticeExtra_0.6-28        Formula_1.2-1              geneplotter_1.48.0        
[37] DESeq2_1.10.1              ggplot2_2.1.0              lambda.r_1.1.7            
[40] Hmisc_3.17-3               scales_0.4.0               splines_3.2.4             
[43] BiocGenerics_0.16.1        GenomicRanges_1.22.4       SummarizedExperiment_1.0.2
[46] xtable_1.8-2               colorspace_1.2-6           acepack_1.3-3.3           
[49] RCurl_1.95-4.8             munsell_0.4.3    

ADD REPLYlink written 18 months ago by Mnoon10

This is strange; must have to do with some package installation or with your connection; have you tried using one of the mirrors as the host, i.e. aisa.ensembl.org, uswest.ensembl.org or useast.ensembl.org?

For me it even works with the same biomaRt and R version. What do you get if you call (in R):

readLines("http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL")

Does it return you lines starting with "TableSet"?

ADD REPLYlink modified 18 months ago • written 18 months ago by Johannes Rainer1.1k

here is the output of mirrors:

> listMarts(host = 'uswest.ensembl.org' )
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> listMarts(host = 'useast.ensembl.org' )
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> listMarts(host = 'asia.ensembl.org' )
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined

here is the output of readLines:

> readLines("http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : too many redirects, aborting ...

Second try:

> ensembl.human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",  host = "www.ensembl.org" )
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

 

@Martin:

In browser, I end up at "http://uswest.ensembl.org/index.html"

It works with 'libcurl', below is the output.

> readLines(url ("http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL", method ="libcurl"))
  [1] " "                                                                                                                                           
  [2] "TableSet\toanatinus_gene_ensembl\tOrnithorhynchus anatinus genes (OANA5)\t1\tOANA5\t200\t50000\tdefault\t2016-02-26 10:04:05"                
  [3] " "                                                                                                                                           
  [4] "TableSet\tcporcellus_gene_ensembl\tCavia porcellus genes (cavPor3)\t1\tcavPor3\t200\t50000\tdefault\t2016-02-26 10:04:18" 

 

ADD REPLYlink written 18 months ago by Mnoon10

It's clear that the server is trying to tell biomaRt something, but not clear what. Try addling verbose=TRUE to listMarts(host="uswest.ensembl.org", verbose=TRUE). It will indicate the command being executed. What happens when you paste that line into a browser? What about readLines? E.g., I have

> xx = listMarts(host = 'uswest.ensembl.org' , verbose=TRUE)
Attempting web service request:
http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
> url = "http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt"
> readLines(url(url, method="libcurl"))
 [1] ""                                                                                                                                                                                                                                                                                                
 [2] "<MartRegistry>"                                                                                                                                                                                                                                                                                  
 [3] "  <MartURLLocation database=\"ensembl_mart_84\" default=\"1\" displayName=\"Ensembl Genes 84\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_ENSEMBL\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"1\" />"          
 [4] "  <MartURLLocation database=\"sequence_mart_84\" default=\"\" displayName=\"Sequence\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_SEQUENCE\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"\" />"                  
 [5] "  <MartURLLocation database=\"ontology_mart_84\" default=\"\" displayName=\"Ontology\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_ONTOLOGY\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"\" />"                  
 [6] "  <MartURLLocation database=\"genomic_features_mart_84\" default=\"\" displayName=\"Genomic features 84\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_GENOMIC\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"\" />"
 [7] "  <MartURLLocation database=\"snp_mart_84\" default=\"\" displayName=\"Ensembl Variation 84\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_SNP\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"1\" />"               
 [8] "  <MartURLLocation database=\"regulation_mart_84\" default=\"\" displayName=\"Ensembl Regulation 84\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_FUNCGEN\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"1\" />"   
 [9] "  <MartURLLocation database=\"vega_mart_84\" default=\"\" displayName=\"Vega 64\" host=\"useast.ensembl.org\" includeDatasets=\"\" martUser=\"\" name=\"ENSEMBL_MART_VEGA\" path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\" visible=\"1\" />"                          
[10] "</MartRegistry>"                                                                                                                                                                                                                                   
ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 20k

http://uswest.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt

When I paste the line in browser I get this error:

Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /biomart/martservice.

Reason: Error reading from remote server

###Using read lines, I get this error.. Basically link seems to be broken or not working as its obvious from above error.

> readLines(url ("http://uswest.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt", method ="libcurl"))
 [1] "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">"                                                                         
 [2] "<html><head>"                                                                                                                 
 [3] "<title>502 Proxy Error</title>"                                                                                               
 [4] "</head><body>"                                                                                                                
 [5] "<h1>Proxy Error</h1>"                                                                                                         
 [6] "<p>The proxy server received an invalid"                                                                                      
 [7] "response from an upstream server.<br />"                                                                                      
 [8] "The proxy server could not handle the request <em><a href=\"/biomart/martservice\">GET&nbsp;/biomart/martservice</a></em>.<p>"
 [9] "Reason: <strong>Error reading from remote server</strong></p></p>"                                                            
[10] "</body></html>"     

 

ADD REPLYlink modified 18 months ago by Martin Morgan ♦♦ 20k • written 18 months ago by Mnoon10

Since this is a problem with Ensembl's biomart, I have forwarded it to helpdesk at ensembl dot org. I will update this post with the response I receive.

ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 20k

The ensembl help desk indicates that they have reverted to a 'last known good' state while they investigate further. Please post here if problems persist.

ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 20k
1

Its working just fine now. Thank you Martin!

ADD REPLYlink written 18 months ago by Mnoon10
0
gravatar for Paul Shannon
18 months ago by
Paul Shannon360
Paul Shannon360 wrote:

biomaRt is now broken for me also.   Following Johannes suggestion:

    readLines("http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL")
    Error in file(con, "r") : cannot open the connection
    In addition: Warning message:
    In file(con, "r") : too many redirects, aborting ...

sessionInfo() 
R version 3.2.4 (2016-03-10) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Oracle Linux Server 7.1 
locale: 
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        

attached base packages: 
[1] stats     graphics  grDevices utils     datasets  methods   base      
other attached packages: 
[1] biomaRt_2.26.1       BiocInstaller_1.20.1 
loaded via a namespace (and not attached): 
 [1] IRanges_2.4.8        parallel_3.2.4       DBI_0.4              
 [4] RCurl_1.95-4.8       Biobase_2.30.0       AnnotationDbi_1.32.3 
 [7] RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1  
[10] stats4_3.2.4         bitops_1.0-6         XML_3.98-1.4  
ADD COMMENTlink written 18 months ago by Paul Shannon360

Where do you end up if you paste the line in your browser? I end up at http://useast.ensembl.org/... and that works if I use that address (useast rather than www) within R. I think this is the preferred solution.

For readLines, I think you can have success by using the 'libcurl' rather than 'internal' method; I don't know if this is available on all platforms

readLines(url("http:/...", method="libcurl"))
ADD REPLYlink written 18 months ago by Martin Morgan ♦♦ 20k
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